The Main Deck is the central area of the B.S.L Research Station in Metroid Fusion. This is the first station that Samus enters when she arrives aboard the station. This area connects the other main sectors via main Elevators. The environment of this area, unlike the other sectors, is not a replica of a section of SR388 or Zebes, though there are some areas that show signs of nature, like the Habitation Deck.
As one of its purposes, the Main Deck is the only area that connects to all other main areas. Aside from these areas, the Main Deck contains many smaller areas within it, each serving a specialized function.
- Main article: Docking Bays
The Docking Bays is an area in the Main Deck where Samus's ship can be accessed. Presumably, this area is dedicated for ship landing.
- Main article: Quarantine Bay
The Quarantine Bay is an area in the Main Deck, where former B.S.L Research Station crew members may have quarantined a feral, X-infected Hornoad. The area seems to be savagely destroyed. The Hornoad's presence here indicates that it may have been the first specimen to have been discovered X-infected aboard the B.S.L Station.
- Main article: Habitation Deck
The Habitation Deck is another area within the Main Deck. This area seemed to keep only the Etecoons and Dachoras. These special creatures may have been singled out as intelligent. Unlike any other area, there appears to be a simple form of entertainment for the creatures that reside in them.
- Main article: Sub-Zero Containment
The Sub-Zero Containment, in direct contrast to the Habitation Deck, is a small prison-like chamber apparently used to hold Ridley and possibly to store other objects in freezing temperature.
- Main article: Reactor Silo
The Reactor Silo is the uncharted area in the Main Deck where the auxiliary power can be activated. The Kihunters made their home here when Nettori and other Sector 2 (TRO) plant life took over the area. The Reactor Core and Auxiliary Station are located within the Reactor Silo.
- Main article: Operations Deck
The Operation Deck is the highest point in the station. The Operations Room is located here, which seems to be the commanding area of the ship. Samus faces a powerful SA-X for a final battle on this deck.
- Main article: Restricted Zone
The map of the Restricted Zone appears only on the Main Deck map, though the two areas are not connected. The Restricted Zone houses the Restricted Laboratory, a secret Metroid program developed by Biologic Space Labs.